Overview

Here are some of the basic concepts, objects, and procedures you need to understand in order to use RCytoscape effectively.

  1. RCy and Cytoscape communicate using XMLRPC, a simple text-only http protocol for calling one program from another, and passing data.

  2. CytoscapeConnection objects connect you to Cytoscape from R, providing the conduit over which requests and data travel

  3. CytoscapeWindow objects extend CytoscapeConnection objects, by adding a graph, a window in Cytoscape, and window-specific commands

  4. It's a good idea to create one CytoscapeConnection object to use for general commands (i.e., commands which are not specific to a particular Cytoscape window)
       cy = CytoscapeConnection ()
   print (version (cy))
   hideAllPanels (cy)
   getWindowList (cy)

  5. Create a graph. (As of this writing (April 2011) RCy supports the Bioconductor graph classes: graphNEL, graphAM, graphBAM. Support for the new MultiGraph class will be available in the next release.) Add nodes and edges, some typical attributes, some visualization rules, display it.

    Please note! Any time you spend studying this example code will serve you well in all subsequent use of RCy! 

    
       # initialize
    g = new ("graphNEL", edgemode = "directed")
    g = initNodeAttribute (g, "nodeType", "char", "undefined")
    g = initNodeAttribute (g, "label", "char", "undefined")
    g = initEdgeAttribute (g, "edgeType", "char", "undefined")

      #   add nodes and edges
    g = addNode ("A", g)
    g = addNode ("B", g)
    g = addNode ("C", g)
    g = addEdge ("A", "B", g)
    g = addEdge ("A", "C", g)

      #  add node and edge attribues
    nodeData (g, "A", "nodeType") = "kinase"
    nodeData (g, "B", "nodeType") = "substrate"
    nodeData (g, 'A', 'label') = 'kinase A'
    nodeData (g, 'B', 'label') = 'substrate B'
    nodeData (g, 'C', 'label') = 'C'

    edgeData (g, "A", "B", "edgeType") = "phosphorylates"
    edgeData (g, "A", "C", "edgeType") = "binds"

      #  create a CytoscapeWindow, after first making sure that no prior window of the same name
      #  name exists already.  (CytoscapeConnections are cheap; create them whenever you need them.)
    cy = CytoscapeConnection ()
    window.title = 'simple test'
    if (window.title %in% as.character (getWindowList (cy)))
      deleteWindow (cy, window.title)
    cw = new.CytoscapeWindow (window.title, g)

      #  send graph to Cytoscape.  this only needs to be done once!
    displayGraph (cw)

      #  ask Cytoscape to layout the graph
    layoutNetwork (cw, 'jgraph-spring')

     #  instruct Cytoscape to use each node's 'label' attribute as the value for the visible label it draws on the node
    setNodeLabelRule (cw, 'label')
     #  experiment on your own, if you wish, with this occasionally useful rule
    setNodeLabelRule (cw, 'nodeType')

     #  slighly more complicated rules.  phosphorylation is a directed activity, so put an arrow only on the substrate end
     #  binding is reciprocal, so put a circle on both ends of that edge

    setEdgeTargetArrowRule (cw, 'edgeType', c ('phosphorylates', 'binds'), c ('Arrow', 'Circle'))
    setEdgeSourceArrowRule (cw, 'edgeType', c ('phosphorylates', 'binds'), c ('None', 'Circle'))

      #  now ask Cytoscape to redraw the graph using these rules
   redraw (cw)

      #  set window and network sizes
   setWindowSize (cw, 600, 400)
   fitContent (cw)
   setZoom (cw, 0.8 * getZoom (cw))

    Don't hesitate to send me questions if you run into trouble: pshannon AT systemsbiology DOT org